[Help] Can a dog get over separation anxiety on his own?

Dog TaxHello /r/DogsI know my request is probably wishful thinking...I hope I do this right. It's hard to search for something so specific... I always feel the need to explain myself before I begin when I post so I'll try to refrain now...IntroI adopted a 3 y/o male neutered Miniature Pinscher Mix on Saturday Evening. He went into his crate easily that day but has increasingly been more stubborn about going back in, but he doesn't whine or anything while in there. I'm doing the 2-week shutdown to the best of my ability. I have to take him on walks for exercise because he won't play with toys (I hope that changes, he started wagging his tail a bit yesterday), and I have no yard.DetailsI've read that shelter dogs are more prone to separation anxiety. Yesterday I had to wash laundry. As soon I stepped out the door he started crying. My boyfriend said that even when I left to talk out the trash earlier he was whimpering but my bf was in the room. I immediately wanted to work on this and rewarded him while he was calm (is this too soon? In an apartment I can't have him yelping all day, nor do I want him stressed). Last night I covered his crate with a blanket, leaving the front open (so he technically can't see me), but I don't know if it's helping with the anxiety. I also went and bought a Thundershirt for him. Today I gave him a ball feeder toy with treats and left the room. I left for 2 minutes without him making a sound but he was definitely alert when I came back and I removed the toy.Dog BackgroundHe seems as though he was abused in his previous home - in the shelter when I lifted the ball to throw he recoiled and winced like he thought I was going to throw it at him or hit him. He doesn't bite but he seems vary wary of sudden movements and loud noises or if you come at him too fast. And the shelter did note his nervousness and shyness. He slowly seems to be gaining more confidence which is part of the reason I wonder if he can resolve his separation anxiety on his own? If he becomes more confident and less anxious in general maybe he will be more calm?The shelter is very nice and, a first for me was they said for the rest of his life, if anything comes up behaviorally I can contact them and they will provide any tips/info/help. So of course if it's unreasonable that it will go away I will contact them because he is an all around perfect dog and I will try to work on this if I have to.TL;DRDog is nervous and shy. Wondering if while he gains more confidence the separation anxiety will subside? Also, could this be something else? I can't imagine what, but it seems so soon. via /r/dogs http://ift.tt/2rDWQFH